title: Activity of the Rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor RpaR.
abstract: The Rhodopseudomonas palustris transcriptional regulator RpaR responds to the RpaI-synthesized quorum-sensing signal p-coumaroyl-homoserine lactone (pC-HSL). Other characterized RpaR homologs respond to fatty acyl-HSLs. We show here that RpaR functions as a transcriptional activator, which binds directly to the rpaI promoter. We developed an RNAseq method that does not require a ribosome depletion step to define a set of transcripts regulated by pC-HSL and RpaR. The transcripts include several noncoding RNAs. A footprint analysis showed that purified His-tagged RpaR (His(6)-RpaR) binds to an inverted repeat element centered 48.5 bp upstream of the rpaI transcript start site, which we mapped by S1 nuclease protection and primer extension analyses. Although pC-HSL-RpaR bound to rpaI promoter DNA, it did not bind to the promoter regions of a number of RpaR-regulated genes not in the rpaI operon. This indicates that RpaR control of these other genes is indirect. Because the RNAseq analysis allowed us to track transcript strand specificity, we discovered that there is pC-HSL-RpaR-activated antisense transcription of rpaR. These data raise the possibility that this antisense RNA or other RpaR-activated noncoding RNAs mediate the indirect activation of genes in the RpaR-controlled regulon.
authors.affiliation: Department of Microbiology, University of Washington, Seattle, Washington 98195-7242, USA.
authors.forename: Hidetada
authors.initials: H
authors.lastname: Hirakawa
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Oda
authors.forename: Somsak
authors.initials: S
authors.lastname: Phattarasukol
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Armour
authors.forename: John C
authors.initials: JC
authors.lastname: Castle
authors.forename: Christopher K
authors.initials: CK
authors.lastname: Raymond
authors.forename: Colin R
authors.initials: CR
authors.lastname: Lappala
authors.forename: Amy L
authors.initials: AL
authors.lastname: Schaefer
authors.forename: Caroline S
authors.initials: CS
authors.lastname: Harwood
authors.forename: E Peter
authors.initials: EP
authors.lastname: Greenberg
mesh_terms: D015107:4-Butyrolactone / Q000031:analogs & derivatives* / Q000378:metabolism; D001426:Bacterial Proteins / Q000378:metabolism*; D018983:DNA Footprinting; D004269:DNA, Bacterial / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D012241:Rhodopseudomonas / Q000502:physiology*; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D014157:Transcription Factors; C088386:homoserine lactone; D015107:4-Butyrolactone